摘要
目的运用免疫信息学技术预测严重急性呼吸综合征冠状病毒2(SARS-CoV-2)的B细胞、细胞毒性T淋巴细胞(CTL)和辅助T(Th)细胞的抗原表位.方法从NCBI数据库检索SARS-CoV-2蛋白序列,根据抗原性≥0.5和氨基酸数≥100进行筛选,最终的蛋白序列用于后续的抗原肽的预测.用蛋白质结构预测软件Phyre2进行三维结构的预测、蛋白质模型结构的细化软件GalaxyRefine优化蛋白的三维结构,最后用蛋白质结构同源建模SWISS-MODEL系统对优化后的结构进行准确性评估.蛋白序列用于CTL、Th细胞和线性B细胞抗原肽预测,三维结构用于结构性B细胞抗原预测.免疫表位数据库和分析资源(IEDB)预测SARS-CoV-2的CTL和Th细胞抗原表位,B细胞线性抗原肽预测软件Bepipred Linear Epitope Prediction 2.0和B细胞结构抗原肽预测软件ElliPro-Epitope prediction based upon structural protrusion分别预测B细胞线性和结构抗原肽.结果从NCBI数据库获得了27个SARS-CoV-2的蛋白序列,去掉抗原性<0.5和氨基酸数<100的蛋白质后,最终选定9个蛋白进行后续抗原肽预测.最终获得了24个CTL、20个Th细胞、12个B细胞线性表位和16个B细胞结构表位.结论获得的抗原表位可用于后续多表位疫苗的设计,相较于只针对单种蛋白靶点的抗原表位而言,多靶点抗原表位具有更强的免疫原性,这些抗原表位对SARS-CoV-2疫苗而言,具有一定的参考价值.
Objective To predict the epitopes of B cells,cytotoxic T lymphocytes(CTL),and T helper(Th)cells of SARS-CoV-2 by immunoinformatics.Methods The SARS-CoV-2 protein sequences were retrieved from NCBI database and screened,and the sequences with antigenicity≥0.5 and amino acid number≥100 were used for epitopes prediction.The Phyre2 server was used to predict the three-dimensional(3D)structure,the GalaxyRefine system to optimize the 3D structure,and the SWISS-MODEL system to evaluate the accuracy of the optimized structure.The CTL,Th cells,and sequential B-cell antigen peptide prediction was based on the sequences of proteins,and the structural B-cell antigen peptide prediction on the 3D structures of proteins.The cytotoxic T lymphocyte(CTL)and Th cell epitopes of SARS-CoV-2 were predicted by the IEDB database.The sequential B-cell antigen peptide prediction and the structural B-cell antigen peptide prediction were performed by BepiPred-2.0:Sequential B-Cell Epitope Predictor and ElliPro-a structure-based tool for the prediction of epitopes,respectively.Results Twenty seven SARS-CoV-2 protein sequences were obtained from the NCBI database.After removing the proteins with antigenicity<0.5 and amino acid number<100,nine proteins were selected for antigen peptide prediction.Finally,24 epitopes from CTLs,20 epitopes from Th cells,and 12 sequential epitopes and 16 structural epitopes from B cells were obtained.Conclusion The epitopes obtained can be used for developing multi-epitope SARS-CoV-2 vaccines.Compared with epitopes that only target a single protein,multi-target epitopes have stronger immunogenicity.These epitopes have certain reference value for the development of SARS-CoV-2 vaccine.
作者
赵健秋
毛燕
董蓉
佟小雅
张茜
查艳
ZHAO Jianqiu;MAO Yan;DONG Rong;TONG Xiaoya;ZHANG Qian;ZHA Yan(Depatment of Nephrology,Guizhou Provincial People’s Hospital,Guiyang 550002;Department of Biomedicine,School of Medicine,Guizhou University,Guiyang 550025;Key Laboratory of Diagnosis and Treatment of Pulmonary Immune Diseases,National Health Commission,Guiyang 550002,China)
出处
《细胞与分子免疫学杂志》
CAS
CSCD
北大核心
2021年第6期487-494,共8页
Chinese Journal of Cellular and Molecular Immunology
基金
贵州省肾脏病临床医学研究中心[黔科合平台人才2201[2020]号]
贵州省高层次创新型人才[黔科合平台人才5636(2018)]
中国医学院中央级公益性科研院所基本科研业务费专项资金(2019PT320003)。
